Computational biology and genomics
A Markov chain is a mathematical system that undergoes transitions from one state to another on a state space in a stochastic (random) manner. Examples of Markov chains include the board game snakes and ladders, where each state represents the position of a player on the board and a player moves between states (different positions…
The Markov Cluster (MCL) Algorithm is an unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Markov clustering was the work of Stijn van Dongen and you can read his thesis on the Markov Cluster Algorithm. The work is based on the graph clustering paradigm, which postulates that natural groups in…
A quick short post on making symmetric matrices in R, as it could potentially be a nasty gotcha. So in R, there are two functions for accessing the lower and upper triangular part of a matrix, called lower.tri() and upper.tri() respectively. Let me illustrate:
Shiny is a package from RStudio that makes it incredibly easy to build interactive web applications with R. Have a look at some of the applications built using Shiny and perhaps you’ll be as impressed as me. I will set up a local Shiny server on Ubuntu (12.04) running under VirtualBox. You don’t actually need…